Package de.jstacs.data

Provides classes for the representation of data.

See:
          Description

Interface Summary
RecyclableSequenceEnumerator This interface extends Enumeration of Sequences by declaring an additional method that allows to reuse the Enumeration.
 

Class Summary
Alphabet Class for a set of symbols, i.e. an Alphabet.
Alphabet.AlphabetParameterSet The super class for the InstanceParameterSet of any Alphabet.
AlphabetContainer The container for Alphabets used in a Sequence, Sample, AbstractModel or ... .
AlphabetContainerParameterSet Class for the AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet of an AlphabetContainer.
AlphabetContainerParameterSet.AlphabetArrayParameterSet Class for the parameters of an array of Alphabets of defined length.
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet Class for the parameter set of an array of Alphabets where each Alphabet may be used for one or more sections of positions.
DiscreteSequenceEnumerator This class enumerates over all Sequences of a specific AlphabetContainer and length.
DNASample This class exist for convenience to allow the user an easy creation of Samples of DNA Sequences.
Sample This is the class for any sample of Sequences.
Sample.ElementEnumerator This class can be used to have a fast sequential access to a Sample.
Sample.WeightedSampleFactory This class enables you to eliminate Sequences that occur more than once in one or more Samples.
SampleKMerEnumerator Class for an RecyclableSequenceEnumerator of Sequences that enumerates all k-mers that exist in a given Sample, optionally ignoring reverse complements.
Sequence This is the main class for all sequences.
Sequence.CompositeSequence The class handles composite Sequences.
Sequence.SubSequence This class handles subsequences.
SequenceEnumeration This class implements a RecyclableSequenceEnumerator on user-specified Sequences.
 

Enum Summary
AlphabetContainer.AlphabetContainerType This enum defines types of AlphabetContainers.
Sample.PartitionMethod This enum defines different partition methods for a Sample.
Sample.WeightedSampleFactory.SortOperation This enum defines the different types of sort operations that can be performed while creating a Sample.WeightedSampleFactory.
 

Exception Summary
EmptySampleException An EmptySampleException will be thrown if no Sequence is in a Sample (i.e. the Sample is empty).
WrongLengthException A WrongLengthException is thrown if a given (sub)sequence length is not correct.
 

Package de.jstacs.data Description

Provides classes for the representation of data.
The base classes to represent data are Alphabet and AlphabetContainer for representing alphabets, Sequence and its sub-classes to represent continuous and discrete sequences, and Sample to represent samples comprising a set of sequences.